The History of African Gene Flow into Southern Europeans, Levantines, and Jews

Priya Moorjani,Joel N Hirschhorn,David Reich,Alon Keinan,Alkes L Price,Edward Burns,Li Hao,Harry Ostrer,Gil Atzmon,Nick Patterson

doi:10.1371/journal.pgen.1001373

Abstract

Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%–3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%–15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%–5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.

Highlights

The history of human migrations from Africa into West Eurasia is only partially understood
We assembled data on 6,529 individuals drawn from 107 populations genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs) (Table S1). This included 3,845 individuals from 37 European populations in the Population Reference Sample (POPRES) [9,10], 940 individuals from 51 populations in the Human Genome Diversity Cell Line Panel (HGDP-CEPH) [11,12], 1,115 individuals from 11 populations in the third phase of the International Haplotype Map Project (HapMap3) [13], 392 individuals who self reported as having Ashkenazi Jewish ancestry from the InTraGen Population Genetics Database (IBD) [14] and 237 individuals from 7 populations in the Jewish HapMap Project [15]
We used HapMap3 Utah European Americans (CEU) to represent Northern Europeans and HapMap3 Yoruba Nigerians (YRI) to represent sub-Saharan Africans, we verified the robustness of our inferences using alternative populations

Summary

Introduction

The history of human migrations from Africa into West Eurasia is only partially understood. Auton et al [8] presented nuclear genome-based evidence for sharing of sub-Saharan African ancestry in some West Eurasians, by identifying a North-South gradient of haplotype sharing between Europeans and subSaharan Africans, with the highest proportion of haplotype sharing observed in south/southwestern Europe. None of these studies used genome-wide data to estimate the proportion of African ancestry in West Eurasians, or the date(s) of mixture. Throughout this report, we use ‘‘African mixture’’ to refer to gene flow into West Eurasians since the divergence of the latter from East Asians; we are not referring to the much older dispersal out of Africa ,45,000 years ago but instead to migrations that have occurred since that time

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Conclusion